Publications

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Preprints

  1. Zhou YC, Structure Conforming Continuum Modeling of Large Protein Comformational Change.
  2. Zhou YC, Diffusion map with sparse sampling.

Journal Articles and Book Chapters

  1. Zhou YC, David Argudo, Frank V. Marcoline, Michael Grabe, A computational model of protein induced membrane morphology with geodesic curvature driven protein-membrane interface, Journal of Computational Physics, 422, 109755, 2020. [DOI] [arXiv]
  2. George Borleske and Zhou YC, Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation, Journal of Computational Physics, 421, 109725, 2020. [DOI] [arXiv]
  3. Zhou YC, On Curvature Driven Rotational Diffusion of Proteins on Membrane Surfaces, SIAM Journal on Applied Mathematics, 80, 359-381, 2020. [DOI] [arXiv]
  4. Zhou YC and Varun Gupta, Interface solutions of partial differential equations with point singularity, Journal of Computational and Applied Mathematics, 362, 400-409, 2019. [DOI] [arXiv]
  5. Aras BS, Zhou YC, Dawes A, and Chou CS, The importance of mechanical constraints for proper polarization and psuedo-cleavage furrow generation in the early Caenorhabditis elegans embryo, PLoS Computational Biology, 14, e1006294, 2018. [DOI]
  6. Swager MR and Zhou YC, Geodesic Curvature Driven Surface Microdomain Formation, Journal of Computational Physics, 345, 260-274, 2017. [DOI] [arXiv]
  7. Wei GW and Zhou YC, Variational Methods for Biomolecular Modeling, in Variational Methods in Molecular Modeling, Springer, 181-221, 2017. [DOI]
  8. Mikucki M and Zhou YC, Curvature-driven Molecular Flow on Membrane Surface, SIAM Journal on Applied Mathematics, 77, 1587-1605, 2017. [DOI] [arXiv]
  9. Mikucki M and Zhou YC, Fast Simulation of Lipid Vesicle Deformation Using Spherical Harmonic Approximation, Communications in Computational Physics, 21, 40-64, 2017. [DOI] [arXiv]
  10. Mikucki M and Zhou YC, Electrostatic Forces on Charged Surfaces of Bilayer Lipid Membranes, SIAM Journal on Applied Mathematics, 74, 1-21, 2014. [PDF] [DOI]
  11. Swager MR and Zhou YC, Genetic Exponentially Fitted Method for Solving Multi-dimensional Drift-diffusion Equations. Molecular Based Mathematical Biology, 1, 26-41, 2013. [PDF] [DOI]
  12. Zhou YC, Electrodiffusion of Lipids on Membrane Surfaces, Journal of Chemical Physics, 136, 205103, 2012. [PDF] [DOI]
  13. Zhou YC, Liu J and Harry D, Matched Interface and Boundary (MIB) Method for Solving Multi-flow Navier-Stokes Equations with Applications to Geodynamics, Journal of Computational Physics, 231, 223-242, 2012. [PDF] [DOI]
  14. Holst M, McCammon JA, Yu Z, Zhou YC and Zhu Y, Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation, Communications in Computational Physics, 11, 179-214, 2012. [PDF] [DOI]
  15. Lu B and Zhou YC, Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-Reaction Rates, Biophysical Journal, 100, 2475-2485, 2011. [PDF] [DOI]
  16. Zhou YC, Lu B and Gorfe AA, Continuum Electromechanical Modeling of Protein-Membrane Interactions, Physical Review E, 82, 041923, 2010. [PDF] [DOI] [Bibtex]
  17. Lu B, Holst M, McCammon JA and Zhou YC, Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions, Journal of Computational Physics, 229, 6979-6994, 2010. [PDF] [DOI]
  18. Zhou YC, Lu B, Holst M and McCammon JA, Continuum Simulations of Acetylcholine Consumption by Acetylcholinesterase: A Poisson-Nernst-Planck Approach, Journal of Physical Chemistry B, 112, 270-275, 2008. [PDF] [DOI]
  19. Lu B, Zhou YC, Holst M and McCammon JA, Recent Progress in Numerical Methods for the Poisson-Boltzmann Equation in Biophysical Applications, Communications in Computational Physics, 3, 973-1009, 2008. [PDF] [DOI]
  20. Zhou YC, Holst M and McCammon JA, Nonlinear Elastic Modeling of Macromolecular Conformational Change Induced by Electrostatic Forces, Journal of Mathematical Analysis and Applications, 340, 135-164, 2008. [PDF] [DOI]
  21. Zhou YC, Feig M and Wei GW, Highly Accurate Biomolecular Electrostatics in Continuum Dielectric Environments, Journal of Computational Chemistry, 29, 87--97, 2008. [PDF] [DOI]
  22. Lu B, Zhou YC, Huber GA, Bond SD, Holst M and McCammon JA, Electrodiffusion: A Continuum-modeling Framework for Biomolecular Systems with Realistic Spatiotemporal Resolution, Journal of Chemical Physics, 127, 135102, 2007. [PDF] [DOI]
  23. Yu SN, Zhou YC and Wei GW, Matched Interface and Boundary (MIB) Method for Elliptic Problems with Sharp-edged Interfaces, Journal of Computational Physics, 224, 729--756, 2007. [PDF] [DOI]
  24. Zhou YC, Wei GW, On the Fictitious-domain and Interpolation Formulations of the Matched Interface and Boundary (MIB) Method, Journal of Computational Physics, 219, 228-246, 2006. [PDF] [DOI]
  25. Zhou YC, Zhao S, Feig M and Wei GW, High Order Matched Interface and Boundary (MIB) Method for Elliptic Equations with Discontinuous Coefficients and Singular Sources, Journal of Computational Physics, 213, 1-30, 2006. [PDF] [DOI]
  26. Sun YH, Zhou YC, Li SG and Wei GW, A Windowed Fourier Pseudospectral Method for Hyperbolic Conservation Laws, Journal of Computational Physics, 214, 466-490, 2006. [PDF] [DOI]
  27. Zhou YC and Wei GW, High Resolution Conjugate Filters for the Simulation of Flows, Journal of Computational Physics, 189, 150-179, 2003. [PDF] [DOI]
  28. Zhou YC, Patnaik BSV, Wan DC and Wei GW, DSC Solution for Flow in a Staggered Double Lid Driven Cavity, International Journal for Numerical Methods in Engineering, 57, 211-234, 2003. [PDF] [DOI]
  29. Guan S, Zhou YC, Wei GW and Lai CH, Controlling Flow Turbulence, Chaos, 13, 64-70, 2003. [PDF] [DOI]
  30. Gu Y, Zhou YC and Wei GW, Conjugate Filters with Spectral-like Resolution for 2D Incompressible Flow, Computers & Fluids, 33, 777-794, 2003. [PDF] [DOI]
  31. Zhou YC, Gu Y and Wei GW, Shock-capturing with Natural High Frequency Oscillations, International Journal for Numerical Methods in Fluids, 41, 1319--1338, 2003. [PDF] [DOI]
  32. Wan DC, Zhou YC and Wei GW, Numerical Solution of Incompressible Flows by Discrete Singular Convolution, International Journal for Numerical Methods in Fluids, 38, 789-810, 2002. [PDF] [DOI]
  33. Yang SY, Zhou YC and Wei GW, Comparison of the Discrete Singular Convolution Algorithm and the Fourier Pseudospectral Method for Solving Partial Difference Equations, Computer Physics Communications, 143, 113-135, 2002. [PDF] [DOI]

Book sections

  1. Zhou YC and Wei GW, High Resolution Conjugate Filters for Hyperbolic Conservation Laws, In: Hou YT and Tadmor E, Eds. Hyperbolic Problems: Theory, Numerics, Applications. Springer-Verlag: Berlin (2002).

Others

  1. Wei GW, Sun YH, Zhou YC and Feig M, Multiresolution Molecular Surfaces [arXiv]